6N7Y

Crystal structure of human FPPS in complex with an allosteric inhibitor MIT-01-102


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XQR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52951.6 M Ammonium phosphate, 20% glycerol, 0.08 M TrisHCl
Crystal Properties
Matthews coefficientSolvent content
2.7755.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.24α = 90
b = 111.24β = 90
c = 77.3γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2017-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1278.6699.80.0470.0490.0140.99923.2133320949.102
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0499.31.3851.4470.4150.8261.911.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4XQR278.6631506164799.620.175440.173930.20244RANDOM73.191
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-3.78-3.787.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.769
r_dihedral_angle_4_deg18.43
r_dihedral_angle_3_deg16.188
r_long_range_B_refined8.248
r_long_range_B_other8.142
r_dihedral_angle_1_deg6.586
r_scangle_other5.753
r_scbond_it3.965
r_scbond_other3.965
r_mcangle_it3.962
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.769
r_dihedral_angle_4_deg18.43
r_dihedral_angle_3_deg16.188
r_long_range_B_refined8.248
r_long_range_B_other8.142
r_dihedral_angle_1_deg6.586
r_scangle_other5.753
r_scbond_it3.965
r_scbond_other3.965
r_mcangle_it3.962
r_mcangle_other3.961
r_mcbond_it2.774
r_mcbond_other2.756
r_angle_refined_deg1.733
r_angle_other_deg1.09
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2657
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing